Pokemon 40,000
by SirVenter
Summary: The Pokemon world has been a part of the Warhammer 40,000 universe for millenia without its denizen's knowledge. The veil is lifted, and war threatens to overwhelm to planet. How will Ash and the others adapt? Who will come out on top? War is coming...
1. Prologue

**Pokemon 40k **

_In the Grim Darkness of the future, there is only war… _

_Prologue:_ During the great crusade of the 31st millennium, the galaxy was conquered and administrated by the imperial forces of Holy Terra, more commonly known as the planet Earth. Many foreign planets were colonized by humanity, who forged thriving settlements even amidst dangerous and sometimes deadly flora and fauna. One such planet was Jerwyk IV, a small blue-green temperate planet similar to old Terra on the outer rim of the galaxy. Jerwyk IV was noted for it's extreme diversity in animal and plant life, with millions of unique species and an entire kingdom not yet recorded in any Xeno-zoologist's record. With regular shipments of supplies from nearby imperial worlds, it seemed that the colonists would have all they needed on their new home.

Then the warp storm hit.

It was by no means a gradual affair; indeed, those manning the communications relays and spacecraft far enough out to witness it often make the claim that the entirety of space turned red in the time it took them to blink. On the surface, little was noticeable save for the infusion of a sweet scent into the air. Over the next hundred years the symptoms of the warp storm would become evident: Amnesia ran rampant among the colonists, wiping out all knowledge of the universe outside of Jerwyk IV within a generation. The new animal kingdom, previously known as Kingdom X, was particularly affected; mutations became abundant, and rapid and pronounced evolution became fairly commonplace. Once life on the planet had stabilized, the citizens gave the bizarre creatures a proper classification: Kingdom Pokemon.

Within five generations, the colonists no longer saw themselves as colonists. They were native residents, born to their world and with no knowledge of the universe beyond it. They soon discovered that most Pokemon had near human level intelligence, and some had significantly more. They trained the animals to work, to fight, to protect, and generally to shore them against the ruin which lurked around every corner. The colonists suffered famine, disease, and a host of other issues tied to the loss of imperial technology. However, through the study of the discarded technological relics of their forefathers, soon the people of Jerwyk were able to establish thriving scientific communities. In particular, the chaotic warp storm that locked them off from the rest of the universe also interacted with the colonists' developments, facilitating the invention of a lightweight portable warp-teleportation device, which functioned with remarkable stability and ease. This technology soon became of common-use in the rapidly diversifying regions of Jerwyk, most ubiquitously in transportation of Pokemon through small devices known as "Pokeballs".

Centuries passed. The various continents of Jerwyk were settled, and thriving cities rose on each. The global sport, if it could be called such, was Pokemon Battling, with each major city sporting a league gym and massive tournaments held on a regular basis. Different regions developed their own independent governments to facilitate local governance, though a relatively peaceful atmosphere was maintained on the planet. Most regions adopted a representative democratic government, though Kanto maintained a unique single-branch system in which the league officials of the region also served as the region's governing officials, with gym leaders joining them in times of crisis.

Millennia passed. Gyms rose and fell in standing, and league champions for each region waxed and waned in popularity. One boy from the back woods of Pallet town met a Pikachu and chased his dream, traveling from region to region and daring any who would to try and stop him. He eventually returned to Kanto and achieved his dream, becoming the league champion and consequently a figurehead of Kanto's society. This is largely his story, though there will be many other players before the end. For warp storms are erratic things; what starts in an instant may last for 10,000 years, and in the blink of an eye it may vanish. Happiness, stability, and peace are all invariably transient states; after all, in the end, there is only war.


	2. To be the very best

_Chapter 1: To be the very best_

Ash Ketchum grinned at Pikachu in the back seat of his limousine. Although he was now the 20-year-old master of the Kanto Pokemon League and one of the biggest figures in the region, he had the expression of the jubilant 12 year old that had just set foot out of Pallet, clad in a slightly fancier version of his previous short-sleeved jacket and black t-shirt combination. One sleeve bore the Pokemon league emblem, with a small crown underneath it to indicate his champion status. Rain was streaming down the windows, the occasional puddle sending a torrent of water up onto the side of the highway between the Indigo Plateau and Cerulean City.

"Pikachu, do you think Togepi's going to be much bigger? And what about her Gyarados; he was always scary, but maybe now he'll be a bit more under control… I can't believe we're going to see her again!" He picked the electric mouse up and gave him a little toss, earning a broad smile and a "Cha!" from Pikachu. The limousine continued to wind down the road, the driver smiling to himself and shaking his head. Ash had been very adamant as to his first official visit as Champion… they were to visit Cerulean City, inspect the gym, and hopefully have a surprise reunion with his old companion Misty.

_Misty…_ Ash sat with a bemused grin, thinking about the fiery water trainer with the sunset hair. They had separated paths years ago, and yet whenever he was alone in the silence of his mind his thoughts traveled to her. He missed the days when she would be behind him, loudly complaining about his utter lack of direction and capacity to get the entire group lost in under a mile of travel. He missed the nights, when the dying embers of their campfire and starlight would illuminate her face, and he would fall asleep to the soft tones of Misty singing to herself. Most of all, he missed waking up each morning with the uncertainty and excitement of a day's adventure ahead of him, knowing that wherever he went his companions would be there to guide and protect him.

The limo passed into a tunnel, which would eventually bring them directly to the outskirts of Cerulean city. Relieved to be out of the storm and eager for a bit of airflow, Ash rolled down his window only to recoil a bit, his noise crinkled. The air smelled wrong… not just the stale musty scent that underground air often carries, but also a distinct souring of the smell. It was as though the air he was breathing was different air, and the young master found himself incredibly unsettled. With muttered request for the driver to go faster, he rolled up the window, trying to convince himself that it was simply a byproduct of the tunnel somehow.

Eventually he pulled to a stop at the Cerulean City Pokemon center. The rain had begun to clear, though there was still a drizzle, and clad in a rain-poncho that concealed most of his face Ash set out for the gym. After standing for a few moments in front of the massive ornamented gate, he pressed the small button marked "Challenger Bell".

"Who goes there!?" Ash's heart skipped a beat as he immediately recognized the voice on the other end. Misty hadn't lost any of her pep, and it sounded like she was intimidating the new trainers as they arrived on their way from Pewter. Rather than inform her of her gym's pending inspection, the raven-haired boy from Pallet decided to have some fun with her.

"Bob Legitt, from Pallet town!" He did his best to raise his voice into a whiny falsetto, doing his best impression of a rookie trainer. "And I'm here to battle you and get my second badge! I'm going to be a Pokemon master!" Ash had to stifle a grin at the sound of his own voice echoing over the intercom. A few seconds later, the gates began to swing open, and Ash turned to signal to the limousine driver down the block with a simple wave of his hand, which the driver responded to with a nod. Striding into the gym, his elation at the prospect of seeing Misty again overrode the lingering unease in his system. Even now, outside of the tunnel… the air just wasn't right.

"So, runt, you think you're good enough to beat me do you?" Misty called out to Ash from a podium on the far end of a large water-themed arena, the cerulean water-droplet emblem etched into the center. Ash dared a glance at her from under the hood of his poncho, almost taken aback by how much she had changed. She still favored jean shorts and her ubiquitous yellow tank tops, but she had grown into a rather fetching beauty. He noted with pride that he was finally taller than her, and smiled to see her hair pulled to the side in the same "Out-of-my-way!" ponytail that she had always kept it in.

"Runt? I thought that was your nickname!" He snickered, reverting to his natural voice. It was quite a bit deeper than she had been used to, but it was still easily close enough for Misty to recognize, together with the glance into his eyes under the hood. Her startled gasp of "Ash!" was cut short as she began flailing to keep her balance, her shock having sent her off-kilter and moments later landing her face first in the pool, a spectacular belly-flop into the water arena which sent Ash to the floor in a fit of laughter.

The tomboyish mermaid easily fished herself out, grumbling as she fought to keep her wet clothes from sticking to her skin, her face flushed crimson with embarrassment. "Ash Ketchum, you slimy little…" She stomped over to him once she had gotten herself situated, rage etched in her features. Just as she was about to smash the boy with her fist, Togepi poked her head out from around the corner and ran furiously in Ash's direction with a squeal of joy, leaping up into his arms with a smile.

"Jeez Togepi, thanks… at least _someone_'s glad to see me…" Ash stuck his tongue out at Misty, tossing back the hood of his poncho now that he had no reason to hide his face.

"I never said I wasn't glad to see you, I just don't think you had to surprise me like that!" She was still seething a bit, but Ash could notice a smile creeping into the corners of her mouth. "So, Pokemon master at last, huh? I guess that means I'm under inspection, to make sure I'm still good enough to be handing out badges. Is that right? Well get ready for a fight, Ash Ketchum, because this isn't my sisters' Cerulean gym!" She tossed a pokeball into the arena behind them, a flash of red and a slight popping sound coming just before the "Staaa!" which announced Starmie's arrival. Ash couldn't help but notice that the pokeball seemed sluggish… as though it was reluctant to send Starmie out. Shaking his head, he chalked it up to exhaustion from the ride over.

"Alright then, but don't say I didn't warn you! Pidgeot, go!" Once again, the red flare and dramatic entrance seemed to be moving in slow motion to Ash. He turned his head to Misty, a look of concern indicating that she had noticed it too. "Maybe the pokeballs just need a tune-up… regardless, we have a fight to get too! Pidgeot, fly up and get ready to dodge!"

Misty cursed to herself; she hadn't even called for an attack, and Ash had predicted her maneuver. A few well-placed water guns from under the pool's surface might've been enough to ground Pidgeot, and then she would have the advantage. "Fine then; if you're going to be a coward, then we'll take the offensive! Starmie, body slam him!" The starfish's center gem glowed bright red with acknowledgment, diving deeper and then suddenly rushing toward the surface.

"Dodge and counter!" At the same time Starmie reached the surface, Pidgeot darted to the side, easily avoiding the water pokemon's trajectory. "Gust her into a wall!" Pidgeot's wings were much stronger than they had been the last time Ash fought Misty… the winds smashed Starmie against the gym wall effortlessly, and kept it pinned in place. Grudgingly, Misty held out the Pokeball and watched as Starmie slowly started turning red… and then moments later, Starmie was safe inside the pokeball.

"That's definitely not normal. What if Starmie had been hurt? I can't keep fighting Ash… it's not safe." Misty looked genuinely scared, and with good reason… sluggish reactions by the pokeballs could make it difficult to get injured Pokemon to medical attention in time. Ash nodded his affirmation, frowning a bit himself.

"Pidgeot, return!" The same return speed applied to Ash's pokeball, with the usual instant transfer taking almost half a minute in total. He couldn't help but notice that for those 30 seconds, the air smelled sweeter, sort of like it had before that afternoon. The two had to be related, and this was over his head… he'd bring it to the labs in Cinnabar after he was done in Cerulean, for analysis. "At least you passed your inspection… going deep and shooting out of the water was your best bet. I just saw it coming."

"Don't gloat, Ash, I'll beat you soon enough!" She did her best to look fierce, but at this point she was shivering where she stood from the cool night air filtering in from the gym's entrance and her sopping wet clothes. Ash gave her an apologetic look, gesturing towards the gym's lobby. "I have a present for you too… but maybe you should wait until you're changed." Her eyes lit up at the mention of a present, suddenly snapping out of her shivers and grinning.

"Oh no, this I have to see. Trying to bribe me for going all these years without a visit?" She followed him down the hallway, leaving small puddles in her wake. "Or maybe you're finally paying me back for my bike… I still haven't forgotten!" He turned to her, still walking down the hallway and fighting back a grin. "Something like that…"

As they turned the corner into the lobby, Misty stopped dead in her tracks. Right in the middle of the room, resting in front of the gym's deserted front desk, was a bright blue _motorcycle_. The body had been detailed with underwater imagery, and above the rear tire was the cerulean gym logo with a pokeball superimposed over the water droplet. Ash smiled and turned to gauge her reaction, opening his mouth. "Misty, I thou-"

He was interrupted by a sudden impact, as the girl practically hurled herself into his arms and pulled him into a tight hug. He could feel his jacket and shirt getting soaked by the wet tank top, sending a bright pink tinge up his chest and into his face. She hadn't hugged him in… well… he couldn't remember her ever hugging him, and certainly not like this. She was trembling, possibly from the cold… it felt odd, feeling her body shake in his arms. "C'mon Misty… you should get changed, you're freezing."

"I'm fine" She retorted, not breaking the embrace. "Ash… thank you. It's beautiful! And I'm sure it'll be perfect for those long distance trips out to vermillion to fish at the harbor." She smiled up at him; still shaking and with a gloss to her eyes which seemed to indicate tears. "Ash… you didn't have to do this for me." She was definitely crying, tears flowing down her face in a steady stream. "I know I probably seemed like it… always asking about the bike… but you didn't ha-"

It was Misty's turn to be cut off. Ash had put a finger to her lips, shaking his head with a bemused grin. As soon as she had quieted, he moved his hand to wipe the tears from her face, his eyes lingering in hers for a moment longer than they had ever dared in the past. "I didn't get it because you bothered me Misty… I got it because I wanted to get you something special. Because it's been so long…" She found herself returning his gaze as though hypnotized, left breathless by the soft touch of his hand.

"So what did you get Brock?" She refused to let herself believe that he honestly thought she was special. She convinced herself that this was just a reunion of the old cadre, and that she was just the first step. But when Ash started stammering, and suddenly avoided her gaze, she knew the truth. "It's just me, isn't it?" She fell silent for several moments, each one sending a progressively darker shade of red into her cheeks. "Why?"

"Misty, I…" He closed his eyes for a moment. This was it… the chance to tell her how he truly felt. How he had felt all along. He hadn't permitted himself to believe it, but he loved her… he loved her! He opened his mouth to let her know… and then paused, as he smelled a sickeningly sweet smell on the air, undoing the recent fouling of the air and then some. _No! No more distractions!_ "Misty, I lo-ARGH!"

A disturbing popping sound rang through the air, akin to the amplified sound of a knuckle being cracked, and behind Ash appeared a creature not-of-this-world. It's skin was a mottled red, banded muscles interrupted only by glaring scars on almost every inch of it's skin. It stood on two legs, much like a human, though instead of feet it had wicked looking talons. Its knees bent backward, much like a dog's, and a jaw filled with razor-sharp teeth split its almost-human face. Its head was topped by a pair of curved horns, and it's hands were gripped around the hilt of a horrific daemonic blade, jagged edges stained with blood tapering up to a razor sharp point, which at the moment was embedded in Ash's side. He coughed once, looked at the blood on his hand, and fell unconscious, two words on his lips escaping as barely a whisper. …_love…you"_


End file.
